Payment types can be restricted by Sales Point Type in the E-Commerce pages. This is done by selecting salespoint types in the Payment Type edit form > Sales Point Type tab in SysManager for each of your payment types, and then setting the value of the SPType key in the site config file to the salespoint type(s) that you want to allow in E-Commerce module.

 

Site Admin Panel > Item Settings > SPType value = 5,10

 

An additional key is used to set the message to display when a guest tries to use a payment type that is not allowed:

 

Site Admin Panel > Checkout Settings > PaymentTypeNotAllowedMsg value = This payment type is not allowed for E-Commerce sales.